Cultivation and quantitative proteomic analyses of acidophilic microbial communities

Journal Article · Fri Jan 01 04:00:00 EST 2010 · The ISME Journal: Multidisciplinary Journal of Microbial Ecology

DOI:https://doi.org/10.1038/ismej.2009.139· OSTI ID:985801

Belnap, Christopher P. ^[1]; Pan, Chongle ^[2]; Verberkmoes, Nathan C ^[2]; Power, Mary E. ^[1]; Samatova, Nagiza F ^[2]; Carver, Rudolf L. ^[3]; Banfield, Jillian F. ^[1]

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1. University of California, Berkeley
2. ORNL
3. Iron Mountain Superfund Facility, Redding

Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 985801
• Journal Information: The ISME Journal: Multidisciplinary Journal of Microbial Ecology, Journal Name: The ISME Journal: Multidisciplinary Journal of Microbial Ecology Journal Issue: 4 Vol. 4
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ABUNDANCE
ACID MINE DRAINAGE
BACTERIA
COMMUNITIES
CULTIVATION
ECOLOGY
FUNCTIONALS
IRON
MODIFICATIONS
OXIDATION
PRODUCTION
PROTEINS
TESTING
acid mine drainage
biofilm
proteomics